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Transcriptome Profiling to Predict Piglet Vitality from Umbilical Cord Blood of Purebreds and Crossbreds born in the Same Litter Comparison of Meishan and Large White Sows Laurianne Canario
V Voillet, N Iannucelli, Y Lippi, P Martin, Y Billon, M SanCristobal and L Liaubet
Session 67. Free communications in genetics
CONTEXT
2/3 of piglet losses in the first 3 days after birth Genetic selection against stillbirth efficient but genetic determinism
different from that of losses during lactation Huby et al.. 2003; Roehe et al 2010
French modern Large White piglets are bigger but less physiologically mature than in the past Canario et al.. 2007
Biological dysfunction may cause lower vitality and higher mortality in early postnatal period
Global gene expression profiling of whole blood validated in human
identify molecular signatures of development at birth Cohen et al 2007
AIM OF THE STUDY
Can transcriptome profiling predict newborn’s survival ability ?
Identify Molecular predictors of piglet level of development at birth and vitality
LW ♀x (½ LW + ½ MS) ♂ MS ♀ x (½ LW + ½ MS) ♂ LW x LW MS x LW LW x MS MS x MS
GENETIC DESIGN Mixture of semen from the 2 breeds First parity sows
Total production 24 MS + 24 LW sows - 3 mixtures of semen Genetic variability maximized Ho: 50% purebred 50 % crossbred piglets / litter
Mobility d0 d1 d3 d7
PHENOTYPIC DATA BIRTH Birth weight W0 Body Length BL BMI and PI
MOBIL 0: no move 1: ½ surface 2: all surface
Growth in early lactation W and ADG d1 d3 d7
LWxLW MSxLW LWxMS MSxMS Total Female 12 9 11 10 42 Male 9 10 11 9 39 Total 21 19 22 19 81
17 sows (3 to 8 piglets per litter) – 3 farrowing batches – 3 mixtures of semen
Agilent 60K microarray
TRANSCRIPTOMIC DATA
BIRTH
* P<0.05 ; ** P<0.01 ; *** P<0.001 ; **** P<0.0001
COMPARISON OF GENOTYPES WITHIN SOW BREED
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EAAP 2016 – SESSION 11 Canario et al.
PIGLET EARLY GROWTH
PIGLET VITALITY
EAAP 2010 Dauberlieu et al.
34.505 spots > differentially expressed probes (DEP) yijk = µ + sexi + genotypej + sexi:genotypej + batchi + mixSemeni + sowk + ε ijk
Benjamini-Hochberg FDR 1 % 2.247 DEP BIC 39 DEP sex : genotype + 228 DEP sex + genotype + 45 DEP sex + 1962 DEP genotype 86 %
DIFFERENTIAL ANALYSES
DISCRIMINANT ANALYSES
sPLS-DA : 10 DEP Axis 1 + 5 DEP Axis 2
GENE ONTOLOGY
PHENOTYPIC-TRANSCRIPTOME CO-VARIATION sPLS
R Software
GENOTYPE x SEX INTERACTION Gene expression
SEPP1 SSC16
Selenium transport Mitochondrial respiratory chain
Cox7b SSCX XIST SSCX
X-inactivation
Is male the weakest sex in LW purebreds ?
Do the differences refer to vitality or merely differences in body composition?
carbohydrate sulfotransferase 9
MNF2 MT
Mitofusin 2, mitochondrial structure
Mitochondrial encoded cytochrome b, Oxydative phosphorylation
CYTB MT
GENOTYPE EFFECT
Clusters of genes that co-vary with growth
LW MSXLW LWXMS MS
Partitioning according to genotype
COVARIATION BETWEEN PHENOTYPE AND GENE EXPRESSION
Relations with vitality at birth?
Body mass indexes Probes and Gene expression
6 genes associated with regulation of immune response (HLA-A)
None gene in common with those found for early growth
NDRG2 negative regulation of cytokine production
LW MSXLW LWXMS MS
Behavioural traits – Probes and Gene expression LW MSXLW LWXMS MS
Mobility at birth Genes related to - muscle mass in mice and locomotor activity in rat - endurance in athletes
What level of expression in the LD muscle?
ACTN2 Alpha actinins - diverse group of cytoskeletal proteins
Behavioural traits – Probes and Gene expression LW MSXLW LWXMS MS
Genes related to bone mineral density, bone structure and bone strength in rat
ARL6IP1 ADP-ribosylation factor-like 6 interacting protein 1 ⇨ Difficulty / inability to walk
From purebreds and crossbreds developped within the same litter Different gene expression according to the 4 genotypes Maternal and paternal influences on piglet development
Some relevant DEG according to genotype x sex Clusters of genes associated with growth, in favour of crossbreds from LW sows
Promising genes related to immunity for BMI and locomotion for early-life behaviour
CONCLUSION
PERSPECTIVES
Survival at risk mainly in LW PB piglets ; include probes from newborn LW PB dead in early postnatal period
Further exploration of genes involved in discrimination and relation to
identified QTL
Integrative approach whole blood + specific tissues Bridging the gap between piglet and fetus dvp in late gestation
Validation studies
Fundings PORCINET project ANR 09 GENM 005 2010-14 PORCIVITA project Animal Genetic Division 2013
GENESI INRA Experimental unit Yvon Billon Jean Bailly Launay Irène Frédéric Meslier William Hebrard Eric Bayle Philippe Epagneaud Philippe Gerbe Jean-Louis Girard Christophe Le Bourhis Cyril Paquet
Cellular Genetic Lab GENPHYSE Toulouse Juliette Riquet Catherine Larzul Nathalie Iannuccelli Maguy Bonnet Christine Lascor Hervé Lagant
Platforms GenoToul (Genopole of Toulouse) GeT Genome for transcriptome: Get-TRiX: Yannick Lippi – Pascal Martin
Thank you for your attention
COMPARISON OF GENOTYPES WITHIN SOW BREED Piglets alive till d7
Higher growth in crossbreds, especially the females from LW sows DATA : 24 sows 282 piglets
Y = genotype * sex + batch + mix + sowID(sow genotype) Lsmeans
Trait Sex LW MSxLW LWxMS MS RSD
W0 (kg) F 1.036 1.155 1.062 0.853 0.095 M 1.279 1.322 1.2101 0.913
LENGTH (cm) F 23.99 s* 24.13 22.99 * 20.85 0.647 M 25.58 25.67 23.73 ** 21.45
BMI (%) F 0.184 0.203 0.207 0.197 0.02 M 0.193 0.203 0.234 0.205
W1 (kg) F 1.102 1.304 ** 1.100 * 0.881 0.061 M 1.364 s**** 1.465 s°° 1.122 0.958
W3 (kg) F 1.400 1.724 **** 1.299 * 1.060 0.074 M 1.689 s**** 1.902 * 1.327 1.159
W7 (kg) F 2.178 2.701 **** 1.972 * 1.604 0.134 M 2.611 s**** 2.928 * 1.992 1.751
COMPARISON OF GENOTYPES WITHIN SOW BREED Piglets alive till D7
No within-genotype difference according to sex No difference in behavioural reactivity
RESU
LTS
PHE
NOTY
PES
Trait Sex LW MSxLW LWxMS MS RSD
ADG03 (kg/d) F 0.117 0.193 0.078 0.074 0.031 M 0.135 0.180 0.035 0.084
ADG07 (kg/d) F 0.374 0.516 * 0.300 0.256 0.048 M 0.440 0.521 0.260 0.282
WGR03 (%) F 0.349 0.5334 **** 0.223 0.285 0.045 M 0.327 0.433 ° 0.236 0.296
WGR07 (%) F 1.116 1.410 ** 0.854 0.947 0.109 M 1.050 1.212 0.857 0.946
MOBIL_d3 F 0.98 1.57 1.01 1.44 0.35 M 1.00 1.57 1.17 1.59
MOBIL_d7 F 1.60 2.22 1.58 1.62 0.24 M 1.78 2.11 1.23 1.63
SampleName GeneName SSC Description [Source:HGNC Symbol]
42412 ATP4B 11 ATPase, H+/K+ exchanging, beta polypeptide
35894 CHST9 6 carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 9
57627 DEGS1 10 degenerative spermatocyte homolog 1, lipid desaturase (Drosophila)
33624 FAM118A 5 family with sequence similarity 118, member A 19158 GRSF1 8 G-rich RNA sequence binding factor 1 53066 MFN2 * mitofusin 2 19923 MT-CO2 MT mitochondrially encoded cytochrome c oxidase II 3187 MT-CYB MT mitochondrially encoded cytochrome b
41722 MT-ND2 MT mitochondrially encoded NADH dehydrogenase 2
13591 PIP4K2A 10 phosphatidylinositol-5-phosphate 4-kinase, type II, alpha
21980 TMPRSS6 5 transmembrane protease, serine 6 60406 MT-ND2 MT 24149 FAM118A 5
ROLE OF PIGLET VITALITY ON SURVIVAL-GROWTH
Characteristics of newborn piglet influencing survival and growth
GENETIC
PHYSIOLOGY X
Birth weight = partial predictor
Level of maturity at birth = major determinant of early survival
Ashworth et al., 2001
BEHAVIOURAL VITALITY
EAAP 2016 – SESSION 11 Canario et al.